DEPOSITING FLUID SPECIMENS ON SUBSTRATES, RESULTING ORDERED ARRAYS, TECHNIQUES FOR ANALYSIS OF DEPOSITED ARRAYS

• US 20040126895A1
• Filed: 05/14/1998
• Published: 07/01/2004
• Est. Priority Date: 01/13/1998
• Status: Abandoned Application

• Current Assignee: Genetic MicroSystems, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Genetic MicroSystems, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: OVERBECK, JAMES W., HONKANEN, PETER, MONTAGU, JEAN I., MACE, MYLES L. Sr., FLOWERS, PETER T.
• Application Number:
  US09/079,324
• Publication Number:
  US 20040126895A1
• Time in Patent Office: Days
• US Class Current: 436/180
• CPC Class Codes: B01J 2219/00364 Pipettes
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01L 3/0244 using pins
• CPC Class Codes: B01L 3/0251 Pin and ring type or pin in tube type dispenser
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 2035/1034 Transferring microquantities of liquid
• CPC Class Codes: G01N 2035/1037 Using surface tension, e.g. pins or wires
• CPC Class Codes: G01N 35/1065 Multiple transfer devices
• CPC Class Codes: G02B 21/0036 Scanning details, e.g. scanning stages
• CPC Class Codes: G02B 21/0048 scanning mirrors, e.g. rotating or galvanomirrors, MEMS mirrors
• CPC Class Codes: G02B 21/0072 details concerning resolution or correction, including general design of CSOM objectives
• CPC Class Codes: G02B 21/0076 arrangements using fluorescence or luminescence
• CPC Class Codes: G02B 21/008 : Details of detection or image processing, including general computer control
• CPC Class Codes: G02B 21/34 : Microscope slides, e.g. mounting specimens on microscope slides
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

Fluid is deposited in spots using supported, compliant pin arragements, supplied by a local reservoir. Pin arragements in the form of reciprocating and rotating devices are shown. Supply of the pins by mobile local subreservoirs limit the range of travel between drop-pickup and drop deposit. Local reservoirs in the form of circular rings and large pins are disclosed. Compliance is achieved by using spring and flexure arrangements. Some embodiments employ planer flexures to mount the pin and constrict its movement. Such deposit techniques are shown used in many analytical, reactive, and productive conditions. Combination of the use of the versatile, high density array or with a flying mini objective, wide field scanning microscope is disclosed. Combination with other sub systems adds to the versatility of the system.

Claims

1. An apparatus for deposit of fluid samples in an array of mutually isolated dots, comprising a deposit device, a fluid source for repeatedly providing a discrete drop of fluid on the deposit device, mechanism for moving the device relatively over an array of spaced apart deposit locations of a receiving substrate, mechanism for repeatedly moving the device, relatively, toward and away from the receiving substrate to deposit respective drops of fluid at respective deposit locations on the substrate by direct contact of drops of fluid on the deposit device with the substrate without direct contact of the deposit device with the substrate.

2. The apparatus of claim 1 in which the deposit device is flexibly mounted and associated with a dampener that enables compliant, dampened contact of the device with the substrate via an intervening film of the fluid.

3. The apparatus of claim 1 or 2 wherein the deposit device is a moveable pin.

18. The apparatus of claim 1 in which the deposit device is mounted on a pair of parallel flexures that maintain the deposit device at a constant angle to a surface on which the drops are deposited.

19. The apparatus of claim 18 in which the parallel flexures are cantivlered and the deposit device is on the free end of the assembly.

20. The apparatus of claim 19 in which at least one of the flexures includes a metal spring element.

21. The apparatus of claim 19 in which at least one of the flexures includes a damping element.

22. The apparatus of claim 21 in which the damping element is a damping layer laminated to a spring layer.

23. The apparatus of claim 22 comprising a lamination of a metal spring layer and a damping layer.

24. The apparatus of claim 22 in which the flexure includes a spring layer laminated on opposite sides of a damping layer.

25. The apparatus of claim 1 in which the deposit device is mounted on a multiple flexure system.

26. The apparatus of claim 25 in which at least one relatively stiff flexure supports the deposit device via at least one intermediate relatively compliant flexure, a driver engaged, effectively, with the relatively stiff flexure, and the deposit device being free to deflect by action of the compliant flexure, upon encountering resistance when moving toward the substrate.

27. The apparatus of claim 1 in which the deposit device is arranged to engage the substrate via a film of the fluid with a pressure less than about 1 gram.

28. The apparatus of claim 1 in which the deposit device has a natural frequency of at least 10 Hz.

29. The apparatus of claim 1 including a cleaning system, and a control system adapted to control relative movement of the deposit device to a depositing relationship to the substrate and a cleaning relationship to the cleaning system.

30. The apparatus of claim 29 in which the deposit device is associated with a local supply device that travels with it, the deposit device and local supply device movable together to the cleaning system.

36. The apparatus of claim ______ in which the deposit device is mounted on a multiple flexure system.

4. The apparatus of claim 1 wherein the fluid source includes a fluid storage device relative to which the deposit device repeatedly moves to resupply the device during the deposit of successive drops.

12. The apparatus of claim 5 constructed to produce relative resupply movement between the deposit device and the local storage device for the deposit of each discrete fluid drop.

31. An apparatus for deposit of fluid samples in a dense array of mutually isolated dots, comprising a deposit device, a fluid source for repeatedly providing fluid to the deposit device, mechanism for moving the device relatively over an array of spaced apart deposit locations of a receiving substrate, mechanism for repeatedly moving the deposit device, relatively, toward and away from the receiving substrate to deposit respective drops of fluid at respective deposit locations on the substrate, and a control system adapted to control relative movement of the deposit device to a deposit relationship with the substrate, wherein the deposit device is mounted on a flexure system which constrains the device to precise motion, and a driver is engaged to drive the deposit device to enable reciprocal motion, constrained by the flexure system, between retracted and extended positions depending upon the position of the driver.

32. The apparatus of claim 31 in which the flexure system is constructed to maintain substantially a constant angle between the deposit device and the substrate as the deposit device approaches the substrate.

33. The apparatus of claim 32 in which the flexure system comprises a pair of parallel flexures.

34. The apparatus of claim 33 in which the flexures are ______.

35. The apparatus of claim 32 in which the flexure system comprises a single flexure.

36-1. An apparatus for deposit of fluid samples in a dense array of mutually isolated dots, comprising at least two deposit pins, at least one fluid source for repeatedly providing a drop of fluid on the end of each deposit pin, mechanism for moving the pins together transversely over an array of spaced apart deposit locations of a receiving substrate, mechanism for repeatedly moving each pin independently, relatively, toward and away from the receiving substrate to deposit respective drops at respective deposit locations on the substrate.

36-3. The apparatus of claim 22 in which at least four such pins and drivers are mounted on a deposit head.

37. The apparatus of claim 35 in which a relatively stiff flexure supports the deposit device via an intermediate relatively compliant flexure, the driver for the device engaged, effectively, with the relatively stiff flexure, and the deposit device being free to deflect relative to the stiff flexure by action of the compliant flexure, upon encountering resistance when moving toward the substrate.

5. The apparatus of claim 4 in which the fluid storage device is a local fluid storage device generally movable over the array of deposit locations, the fluid storage device being constructed and arranged to resupply the deposit device at various locations with respect to the array.

6. The apparatus of claim 5 in which the local fluid storage device and the deposit device are coupled for transverse motion across the array.

38. An apparatus for deposit of fluid samples in a dense array of mutually isolated dots, comprising a deposit pin, a fluid source for repeatedly providing a drop of fluid on the end of the deposit pin, mechanism for moving the pin relatively over an array of spaced apart deposit locations of a receiving substrate, mechanism for repeatedly moving the pin, relatively, toward and away from the receiving substrate to deposit respective drops at respective deposit locations on the substrate, and wherein the pin is mounted on a flexure system which constrains the pin to a predetermined path of travel, and a driver is engaged to drive the pin to enable reciprocal motion, constrained by the flexure system, between retracted and extended positions depending upon the position of the driver.

39. The apparatus of claim 38 in which a member defines a generally annular fluid retention surface, and the deposit pin is constructed to move within the annular retention surface from retracted to extended positions, in the retracted position the deposit end of the pin being retracted from the lower surface of fluid retained by the annular surface of the storage device, and in the extended position the deposit end of the pin being projected beyond the lower surface of the retained fluid.

37-2. The apparatus of claim 36 constructed to mount a number of microscope slides to serve as said substrate in deposit-receiving relationship, and a control system constructed and arranged to move the deposit pins in the manner to form deposits on more than one slide.

37-4. A deposit mechanism for deposit of biological fluid dots in an array, comprising a pin supported by a flexure, a source of biological fluid for deposit, and a driver engaged to drive the pin to enable reciprocal motion constrained, between retracted and extended positions depending upon the position of the driver.

38-5. The apparatus of claim 37 including a discrete local fluid supply for the pin.

40-7. The apparatus of claim 46 in which the local supply device is driven to enter a supply well and having a surface adapted to retain a supply of fluid by surface tension or capillar effects.

41-8. The apparatus of claim 40 in which a retaining surface of the local supply has surface roughness of at least 1000 microinch.

42-9. The apparatus of claim 41 in which a member has an inner annular surface having the surface roughness.

43-6. The apparatus in which two or more deposit pins according to claim 39 are grouped together for movement by a single drive as a corresponding member of members defining annular fluid retention surfaces according to claim 39 are associated respectively with respective pins, the members driven by a single drive member.

43-10. The apparatus of claim 44 in which the member has an outer surface that is by ______.

44-11. The apparatus of claim 41 sized and constructed to enter a well of a PCR plate and extract fluid by surface position or capillary efforts for supply to the deposit device.

45. The apparatus of claim 44 wherein the source includes a fluid storage device relative to which the deposit device repeatedly moves to resupply the device during the deposit of the isolated drops of fluid.

7. The apparatus of claim 6 in which the local fluid storage device and the deposit device are decoupled for movement toward and away from the substrate.

8. The apparatus of claim 5 in which the local storage device is constructed and arranged to be replenished from a remotely located relatively large reservoir.

9. The apparatus of claim 8 in which the reservoir is constructed to store a multiplicity of isolated fluid volumes, the apparatus constructed to move the local supply device to a selected fluid volume of said reservoir for replenishment.

10. The apparatus of claim 9 in which the volumes comprise the wells of a plate and the local storage device is constructed to dip into the well.

11. The apparatus of claim 10 in which the local storage device has a fluid retaining surface having a surface roughness of at least 1000 microinch.

13. The apparatus of claim 5 in which the deposit device is a moveable pin and the local storage device includes a member which defines a generally annular fluid retention surface, and the deposit pin is constructed to move within the annular retention surface from retracted to extended positions, in the retracted position the deposit end of the pin being retracted from the lower surface of fluid retained by the annular surface of the storage device, and in the extended position the deposit end of the pin being projected beyond the lower surface of the retained fluid.

14. The apparatus of claim 13 in which the annular surface is generally aligned with the pin and a driver is associated with the member that defines the annular surface to move the member generally linearly downwardly beyond a position of a deposit end of the pin to a replenishment position, the pin and the member defining the annular surface and associated drivers being movable to the cleaning system, and to a replenishment region in which the annular member is replenished.

15. The apparatus of claim 1 in which the deposit device is mounted on a flexure which constrains the device to a predetermined path of travel, and a driver is engaged to cause reciprocal motion constrained by the flexure, between retracted and extended positions depending upon the position of the driver.

16. The apparatus of claim 1 in which a stable spring is arranged to urge the deposit device in the direction opposite to the deposit motion.

40. The apparatus of claim 39 in which a driver is arranged to move the annular member generally downwardly beyond the deposit end of the pin to a replenishment position.

41. The apparatus of claim 40 in which the flexure-mounted pin and the member defining on annular retention surface are associated with respective drivers.

42. The apparatus of claim 40 in which the pin and member are movable as an assembly to a station for cleaning, and to a replenishment region in which the member is replenished from a selected source.

43. The apparatus in which at least four pin and annular member assemblies according to claim 40 are clustered for movement together transversely over the substrate.

44. An apparatus for deposit of fluid samples in a dense array of mutually isolated dots, comprising a deposit device, a source of fluid for the deposit device, mechanism for moving the deposit device relatively over an array of spaced apart deposit locations of a receiving substrate, mechanism for repeatedly moving the deposit device, relatively toward and away from the receiving substrate to deposit respective drops of fluid at respective deposit locations on the substrate, a cleaning system, and a control system adapted to control relative movement of the deposit device between a resupply relationship to the source, a depositing relationship to the substrate and a cleaning relationship to the cleaning system.

46. The apparatus of claim 45 in which the fluid storage device is a mobile local fluid storage device generally movable with the deposit device over the array of deposit locations, the fluid storage device being constructed and arranged to locally resupply the deposit device during its deposit sequence.

47. The apparatus of claim 46 in which the local storage device is constructed and arranged to be replenished from a remotely located relatively large reservoir.

48. The apparatus of claim 47 in which the reservoir is constructed to store a multiplicity of isolated fluid volumes, the apparatus constructed to move the local supply device to a selected fluid volume of said reservoir for replenishment.

49. The apparatus of claim 47 constructed to produce relative resupply movement between the deposit device and the local storage device for the deposit of each discrete drop.

50. The device of claim 45 or 49 constructed to prepare a series of slides in identical manner, the carrier constructed to hold a series of slides, and the control system constructed to deposit a drop of a given composition upon identical locations on the series of slides, by respective movements of the head.

51. The device of claim 50 in which the deposition head comprises a multiplicity of said deposit pins ganged to form a multiplicity of drops.

52. The device of claim 50 in which the deposit pins are associated with respective discrete drivers.

53. The device of claim 51 in which the deposit pins are associated with a single driver.

54. The device of claim 45 wherein the deposition head comprises an annular supply ring constructed to be immersed in and withdrawn from a well of a sample-containing reservoir to retain between wall portions of the annular ring a supply of fluid carrying material to be examined, the deposit pin being operative within the annular ring to move generally axially between a retracted position in which a deposit end of the pin is withdrawn above an exposed surface of the retained sample, and an extended position in which a dot of the fluid is carried on the end of the pin for deposit on the slide.

55. The device of claim 45 or 54 in which the deposit pin is mounted on at least one flexure that constrains the deposit pin to a predetermined path of travel relative to the head.

62. The apparatus of claim 54 or 45 in which over-travel of the driver of the pin toward the receiving surface is permitted by the weak spring without significant effect upon the spacing of the end of the pin from the receiving surface.

45-12. Apparatus for automated preparation of a microscope slide, comprising a microscope slide holder, a carrier operative over a slide on the holder, and a deposition head mounted on the carrier, the deposition head including a deposit pin constructed to carry a drop of fluid from a fluid supply, and mechanism constructed, in a deposit sequence, to move the deposit pin relative to the supply to pick up a drop of fluid, and move the deposit pin toward the microscope slide to completely deposit the drop of fluid on the slide, there being a control system arranged to repeat the deposit sequence to produce a high density of drops of deposited fluid upon the slide.

46-13. The device of claim 45 in which the deposit pin has a deposit end comprising an abrupt profile that defines the perimeter of the drop of fluid to be picked up.

47-14. The device of claim 46 in which the pin comprises a generally cylindrical shaft and an end rim.

48-15. The deposition head of claim 47 in which the end rim is defined by a generally planar butt end of the pin.

49-16. The device of claim 45 wherein the supply comprises a sub-reservoir mounted on the head, closely adjacent to the deposit pin.

56. Apparatus for deposit of fluid samples in a dense array of mutually isolated dots on a receiving surface comprising a deposit pin, a fluid source for repeatedly providing a drop of fluid on the end of the deposit pin, mechanism for moving the pin relatively over an array of spaced apart deposit locations of a receiving substrate, mechanism for repeatedly moving the pin, relatively, toward and away from a targeted point on the receiving substrate to deposit respective drops of fluid at respective deposit locations on the receiving surface, and means for stopping movement of the depositing pin toward the targeted point on the receiving surface while fluid remains between the end of the pin and the receiving surface.

57. The apparatus of claim 56 in which said means comprises a compliant system that limits the motion of the pin in response to resistance force transmitted to the pin.

58. The apparatus of claim 57 in which the resistance force is predetermined to be less than the total displacing force required to cause the pin to displace the fluid so much that the pin makes solid contact with the receiving surface.

59. The apparatus of claim 56 in which a spring system mounting the deposit pin limits the force with which the deposit pin presses toward the receiving surface.

60. The apparatus of claim 59 in which the deposit pin is coupled to the driver by a weak spring of selected spring value.

61. The apparatus of claim 60 in which the strength of the spring is selected to enable the deposit pin to cease movement toward the receiving surface before termination of movement of the driver.

63. The apparatus of claim 57 in which the compliant system including a leaf spring or flexure.

64. The apparatus of claim 60 in which the weak spring is supported on a relatively stiff spring engaged by the driver for moving the deposit pin.

65. An apparatus comprising a deposit pin constructed and arranged to deposit a first dot upon a substrate and thereafter, in registration, to deposit a second dot upon the first dot.

66. The apparatus of claim 65 in combination with a source of multiple fluids comprising a first fluid for said first dot and a second fluid for the second dot, the first and second fluids selected to potentially interact.

67. The apparatus of claim 65 including a device for depositing a large spot of a given reagent and a device for depositing dots of smaller size of different reagents upon the deposited large dot.

68. A fluid deposit arranger for transferring a drop of fluid to a substrate by engaging the drop with the substrate, the device mounted on a compliant spring for compliant engagement with the substrate and incorporating a motion damping member.

69. The fluid deposit arranger of claim 68 in which the spring comprises a flexure mounting.

70. The arranger of claim 69 in which at least one portion of the flexure mounting comprises a composite in which a layer of flexible damping material is bonded to a flexure member.

71. The arranger of claim 70 in which a pair of flexure members are bonded together in a composite sandwich containing a layer of damping material.

72. The arranger of claim 70 in which the flexible damping layer comprises a rubber or rubber-like compound.

73. The arrayer according to claim 71 in which at least one of the flexure layers of the composite is a resilient plastic layer.

74. The arrayer according to claim 73 in which at least one of the flexure layers comprise polyamide.

75. The arrayer according to claim 71 in which one of the flexure layers comprises a spring metal and the other layer comprises a bonding material having damping characteristics.

76. The arrayer according claim 69 in which the flexure is a planar flexure about 8 mm in width and between about 20 and 25 mm in length.

77. The arrayer according to claim 71 in which a layer of flexible resin is laminated by rubber cement to a flexible metal layer.

78. The arrayer of claim 68 in which a deposit pin is mounted upon a pair of parallel flexures.

79. The array of claim 78 in which at least one of the flexures comprises spring metal, and the other comprises, at least in part, a material having greater dampening properties than said spring metal.

80. The arrayer of claim 78 in which both parallel flexures comprise a sandwich according to claim 77.

81. The arrayer of claim 68 having a natural frequency greater than about 10 HZ.

82. A deposit head including at least two flexure mounted pins, and a single actuator arranged to move the pins simultaneously from supply to deposit positions, the head mounted for lateral movement in both X and Y axes.

83. The deposit head of 82 in which the pins are spaced apart 9 mm.

84. A deposit head including at least two flexure mounted pins, each associated with its own actuator to be moved independently from supply to deposit position, the head mounted for lateral movement in both X and Y axes.

85. The deposit head of claim 84 in which the pins are spaced apart 9 mm.

86. An aliquot carrier defining a fluid-retaining aperture through which a deposit device can transit to pick up a drop of fluid to be deposited, internal surfaces defining said aperture having a surface roughness that increases its wettability.

17. The apparatus of claim 1 in which the deposit device is constrained in its path of motion by at least one planar flexure.

87. The carrier of claim 86 in which the surface roughness is produced by a technique selected from the class of sanding, broaching, machining, screw or knurl forming, coating or forming the surface of particles that provide surface roughness as by sintering or molding.

87-17. The carrier of claim 86 in which the surface roughness is at least 100 microinch.

88. A process of printing comprising, under computer control, moving at least one flexure mounted pin to selected X,Y positions, and depositing with said pin, a desired material.

89. The method of claim 88 in which the material is an ink or dye.

90. The method of claim 89 in which the material is a photoresist material.

91. The method of claim 88 in which the material is a varnish or encapsulant.

92. A method of causing a biological compound to interact with another substance at a predetermined position on a substrate the step comprising depositing at least one of the compound or reagent in a precisely determined localized spot relative to the substrate by mechanically lowering a compliant pin, to which a drop of the compound or reagent is adhered by surface tension, toward the substrate until the drop contacts the substrate or a pre-applied compound on the substrate with the pin executing a controlled force of less than a gram thereon, and thereafter mechanically lifting the pin away from the substrate under conditions in which the fluid drop transfers to the substrate or the pre-applied compound on the substrate.

93. The method of claim 92 in which drops of both the compound and the other substance are successively deposited by the technique of claim 92.

94. The method of claim 92 in which the pin, when approaching the substrate, applies a force to the substrate with a force of abouth 0.5 grams.

95. The method of claim 92 in which the compliant pin is mounted upon a support by flexures that constrain the pin to substantially linear motion relative to the support, and moving the support carrying the flexures and pin toward the substrate in an overtraveling linear motion parallel to the direction to which the pin is constrained to deflect, during which motion the pin engages the substrate or pre-applied compound on the substrate, and the flexures deflect in response to resistance encountered by the pin, thereby cushioning the contact of the pin.

96. The method of claim 92 in which a supply of the biological compound or substance to be deposited by the pin is supported above the substrate at the deposit location within a ring by surface tension, and the pin is lowered through the ring in the manner that a relatively small drop of the reagent from the supply is adhered to the end of the pin by surface tension.

97. The method of claim 92 in which the fluid to be deposited from fluid selected the group of fluids described in the specification.

98. The method of depositing a biological fluid with a pin comprising supporting fluid within a ring by surface tension, and the pin is lowered through the ring in the manner that a relatively small drop of the reagent from the supply is adhered to the end of the pin by surface tension.